I cannot reproduce daily build failures found in the trena package by the build system. The build report shows:
trena RUnit Tests - 86 test functions, 7 errors, 0 failures ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_bugInStartEndOfMinusStrandHits: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_findMatchesByChromosomalRegion: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_findMatchesByChromosomalRegion.twoAlternateAlleles: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_findMatchesByMultipleChromosomalRegions: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_getSequence: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_noMatch: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed This seems similar to a bioc support exchange from two years ago, which may suggest that the build system's BSgenome.Hsapiens.UCSC.hg38 is the locus of the problem. I offer suggestion very tentatively. support https://support.bioconductor.org/p/95963/ Any suggestions? - Paul sessionInfo() # from my clean R CMD check R version 3.6.0 beta (2019-04-11 r76379) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS Matrix products: default BLAS: /local/users/pshannon/src/R-beta/lib/libRblas.so LAPACK: /local/users/pshannon/src/R-beta/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] RPostgreSQL_0.6-2 DBI_1.0.0 RUnit_0.4.32 [4] trena_1.5.14 MotifDb_1.22.0 Biostrings_2.48.0 [7] XVector_0.20.0 IRanges_2.14.12 S4Vectors_0.18.3 [10] BiocGenerics_0.26.0 glmnet_2.0-16 foreach_1.4.4 [13] Matrix_1.2-17 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.10.1 lassopv_0.2.0 [3] progress_1.2.0 lattice_0.20-38 [5] rtracklayer_1.40.6 blob_1.1.1 [7] XML_3.98-1.19 rlang_0.3.4 [9] flare_1.6.0 BiocParallel_1.14.2 [11] bit64_0.9-7 splitstackshape_1.4.8 [13] matrixStats_0.54.0 GenomeInfoDbData_1.1.0 [15] stringr_1.4.0 zlibbioc_1.26.0 [17] codetools_0.2-16 memoise_1.1.0 [19] Biobase_2.40.0 biomaRt_2.36.1 [21] GenomeInfoDb_1.16.0 curl_3.3 [23] AnnotationDbi_1.42.1 lars_1.2 [25] Rcpp_1.0.1 BSgenome_1.48.0 [27] DelayedArray_0.6.6 org.Hs.eg.db_3.6.0 [29] bit_1.1-14 Rsamtools_1.32.3 [31] BSgenome.Hsapiens.UCSC.hg38_1.4.1 RMySQL_0.10.17 [33] hms_0.4.2 digest_0.6.18 [35] stringi_1.4.3 GenomicRanges_1.32.7 [37] grid_3.6.0 tools_3.6.0 [39] bitops_1.0-6 magrittr_1.5 [41] RCurl_1.95-4.12 RSQLite_2.1.1 [43] randomForest_4.6-14 crayon_1.3.4 [45] vbsr_0.0.5 pkgconfig_2.0.2 [47] MASS_7.3-51.4 data.table_1.12.2 [49] prettyunits_1.0.2 httr_1.4.0 [51] assertthat_0.2.1 iterators_1.0.10 [53] R6_2.4.0 GenomicAlignments_1.16.0 [55] igraph_1.2.4.1 compiler_3.6.0 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel